Australian Institute of Marine Science

Background The wild stocks of Pinctada maxima pearl oysters found off the coast of northern Australia are of critical importance for the sustainability of Australia’s pearling industry. Locations inhabited by pearl oysters often have oil and gas reserves in the seafloor below and are therefore potentially subjected to seismic exploration surveys. The present study assessed the impact of a simulated commercial seismic survey on the transcriptome of pearl oysters. Animals were placed at seven distances (-1000, 0, 300, 500, 1000, 2000, and 6000 m) from the first of six operational seismic source sail lines. Vessel control groups were collected before the seismic survey started and exposed groups were collected after completion of six operational seismic sail lines (operated at varying distances over a four-day period). Samples from these groups were taken immediately and at 1, 3, and 6 months post-exposure. RNA-seq was used to identify candidate genes and pathways impacted by the seismic noise in pearl oyster mantle tissues. The quantified transcripts were compared using DESeq2 and pathway enrichment analysis was conducted using KEGG pathway, identifying differentially expressed genes and pathways associated with the seismic activity. Results The study revealed the highest gene expression and pathway dysregulation after four days of exposure and a month post-exposure. However, this dysregulation diminished after three months, with only oysters at -1000 and 0 m displaying differential gene expression and pathway disruption six months post-exposure. Stress-induced responses were evident and impacted energy production, transcription, translation, and protein synthesis. Conclusion Seismic activity impacted the gene expression and pathways of pearl oysters at distances up to 2000 m from the source after four days of exposure, and at distances up to 1000 m from the source one-month post-exposure. At three- and six-months post-exposure, gene and pathway dysregulations were mostly observed in oysters located closest to the seismic source at 0 and − 1000 m. Overall, our results suggest that oysters successfully activated stress responses to mitigate damage and maintain cellular homeostasis and growth in response to seismic noise exposure.

Although global warming is leading to more frequent mass coral bleaching events worldwide, parts of the Great Barrier Reef (GBR) have consistently escaped severe coral bleaching. Modeling and satellite observations show that climate refugia are created by the upwelling of cooler water to the surface through the interactions of tides and currents with dense reef structures. Here, we use a high-resolution nested regional ocean model to investigate the future status of two relatively large refugia. On the basis of model projections under a high-emission scenario, we find that the upwelling mechanisms will stay active in a warming climate, and these regions are likely to remain approximately more than 1°C cooler than surrounding waters until at least into the 2080s, providing thermal relief to corals. Identification and protection of these refugia may help facilitate reef survival and related biodiversity preservation by allowing their corals time to acclimatize and adapt and ultimately provide source populations to replenish the rest of the reef.

Marine heatwaves are intensifying under climate change, exposing populations of reef-building corals to mass mortality and intense selective pressure. It remains unknown whether adaptation can keep pace with warming and maintain reef functioning. We have developed an eco-evolutionary metapopulation model for Acropora , an ecologically important yet highly threatened coral taxon. We find that although corals have some adaptation capacity, they will suffer severe heatwave-induced declines over the coming decades. For a future where emissions lead to ~3°C of global warming, natural selection could allow populations to persist, albeit in severely depleted states with elevated extinction risk and potential loss of ecosystem functioning. Yet, for thermally sensitive coral populations to thrive post-2050 demands rapid reductions of greenhouse gas emissions that limit global warming to 2°C.

Epilithic algae dominate cover on coral reefs globally, forming a critical ecological interface between the benthos and reef organisms. Yet, the drivers of epilithic algal composition, and how composition relates to the distribution of key taxa, remain unclear. We develop a novel metric, the Epilithic Algal Ratio, based on turf cover relative to total epilithic algae cover, and use this metric to assess cross-scale patterns. We reveal water quality and hydrodynamics as the key environmental drivers of the Epilithic Algal Ratio across the Great Barrier Reef (GBR), and reefs globally. On the GBR, the abundance of herbivorous fishes and juvenile corals were also related to the Epilithic Algal Ratio, suggesting that reefs with long-dense turfs support fewer herbivores and corals. Ultimately, epilithic algae represent the interface through which the effects of declining water quality, which impacts a third of reefs globally, can reverberate up through coral reefs, compromising their functioning.

High-latitude coral reefs (HLCRs) are unique ecosystems with diverse biological assemblages, including many low latitude species on their distribution margins. These ecosystems are threatened by fisheries exploitation, habitat destruction and climate change; however, relative to low latitude coral ecosystems, our understanding of their structure and functioning is limited. This is particularly true for sharks and rays. In this study, we used baited remote underwater stereo-video systems to determine the effect of habitat and management on the assemblage structure of elasmobranchs on the HLCRs of southern Africa (26-28°S; iSimangaliso Marine Protected Area [MPA], South Africa, and the adjoining Ponta do Ouro Partial Marine Reserve, Mozambique). We recorded a total of 12 species of shark (142 individuals) and 9 species of ray (40 individuals) over 2 brief time frames (November 2016 and June 2017). All species were tropical with many on the southern limit of their known distributions. Sharks increased in diversity with depth and showed a preference for the reef and mosaic habitats, relative to sand. The occurrence of rays was predominantly influenced by the presence of low relief habitats. These findings highlight the need for MPAs to encompass both sand and reef habitats over broad depth ranges to effectively protect elasmobranch assemblages. We found evidence to support the high average abundance and diversity of sharks and rays within MPAs of South Africa and southern Mozambique. The results highlight the importance of marginal HLCRs, particularly those within MPAs, for the management and conservation of tropical elasmobranch species.

Fertile hybrids can enhance the adaptive capacity and resilience of species under stress by increasing genetic diversity within populations, masking the effects of deleterious recessive alleles, and facilitating the introgression of beneficial genetic variants into parental species. However, many hybrids are infertile. We compared the fertility of aquarium‐reared F1 hybrid and purebred corals of the species Acropora loripes and Acropora kenti and examined the viability of early life stages of second‐generation (F2) hybrid and back‐crossed planula larvae and recruits. The F1 hybrids spawned viable gametes and the F2 hybrid and back‐crossed embryos developed into planula larvae and settled to become sessile coral recruits. The F1 hybrids had greater reproductive fitness than the F1 A. loripes purebred stock in an aquarium environment based on their probability of spawning and their fertilization success in crosses using their gametes. Interspecific coral hybrids can therefore be fertile and have high reproductive fitness, which could benefit the persistence of threatened coral reefs.

Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential. Results We present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids, Acropora palmata and A. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genus Acropora exhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from one A. palmata family and 16 A. cervicornis families using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM for A. palmata and A. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps. Conclusions Together, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the Atlantic Acropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Small volumes of water containing environmental DNA (eDNA) are increasingly combined with metabarcoding to generate biodiversity data for specific fractions of marine flora and fauna. To date, however, few studies have utilized this technique to assess how well it captures seasonal patterns in coral reef communities or how environmental and methodological factors influence eDNA detections. In our study, we used three eDNA metabarcoding assays primarily targeting bony fish and elasmobranchs, as well as cnidarians and sponges (Cnidaria/Porifera) combined with monthly seawater sampling to (1) investigate temporal variation in taxonomic detections and (2) statistically test the potential effect of season, sea surface temperature, timing of spawning (using moon phase as a proxy), and sample preservation on taxon detection across a 12-month period in a model coral reef system (Big Vicki’s Reef, Lizard Island, Great Barrier Reef, Australia). Species-level fish and genus-level scleractinian coral detections from standardized visual surveys conducted at the same coral reef, in addition to a curated list of all known fishes recorded from the more expansive coral reef system across 46 years, were used to validate eDNA detections. Our eDNA dataset indicated that the number of taxa detected were consistently highest in September for fish, and in February followed by September for Cnidaria/Porifera. Conversely, detections were lowest in June and July for all taxa. Some, but not all, of the environmental and methodological variables explained the observed temporal pattern in biological communities or systematic changes in the number of taxa, and in some cases, this effect was taxon dependent. Our study also highlights the significance of timing in eDNA biodiversity surveys conducted on tropical coral reefs in the Southern Hemisphere. To obtain the most meaningful estimates of site diversity, we recommend focusing sampling efforts between early spring and early autumn. Alternatively, allocating an entire year to sampling would better capture seasonal variation and provide more comprehensive insights into coral reef biodiversity.

Coral reef fisheries support livelihoods and provide an affordable source of essential dietary nutrients to coastal people. However, climate‐driven coral bleaching is dramatically altering reef habitats and changing reef fish composition, diversity, and productivity. We used data from fisheries independent surveys and artisanal trap landings to explore how reefs with different responses to coral bleaching differed in habitat configurations, fisheries catch rates, economic returns, and nutritional content. Coral‐associated fishes supported the highest catch rates, greatest species diversity, highest rates of economic returns for fishers, and a wide price range for consumers. Macroalgae‐associated fishes supported the greatest overall fisheries yields, which indicated higher fishery dependence on these habitats. Nutrient content was high in catches across all habitats, but concentrations varied by nutrient, which suggested that fishing across a range of reef habitats should provide the greatest variety of nutrients to coastal communities.

Marine heatwaves are becoming more frequent during summer and pose a significant threat to coral reef ecosystems. Restoration efforts have the potential to support native coral populations and guard them against some degree of environmental change, while global action against climate change takes place. Interspecific hybridization is one approach through which resilient coral stock could be generated for restoration. Here we compared the performance of Acropora kenti and A. loripes hybrid and purebred coral recruits under a simulated thermal stress event. A. kenti eggs were successfully fertilized by A. loripes sperm to produce 'KL' hybrids, but no 'LK' hybrids could be produced from A. loripes eggs and A. kenti sperm. Despite corals in the elevated treatment accruing thermal stress (>12 degree heating weeks over 2 months) known to result in mass bleaching, both purebred and hybrid recruits showed no signs of stress under the simulated temperature regime, based on the performance indicators survivorship, size, color (a proxy of bleaching), and photochemical efficiency of photosystem II. Comparisons between the hybrids and purebreds studied here must be interpreted with caution because hybrid sample sizes were small. The hybrids did not outperform both of their purebred counterparts for any metrics studied here, demonstrating that there are limitations to the extent to which interspecific hybridization may boost the performance of coral stock. In general, the purebred A. loripes recruits performed best under both ambient and elevated conditions. The performance of the KL hybrid corals was similar to the maternal parental species, A. kenti, or not significantly different to either parental purebred species. The Symbiodiniaceae communities of the KL hybrids were characteristic of their maternal counterparts and may have underpinned the performance differences between the A. kenti/KL hybrid and A. loripes recruits.

Assisted coral recovery (ACR) initiatives are establishing rapidly in coral reefs worldwide, using a variety of devices and techniques. In the Great Barrier Reef (GBR, the Reef), site-scale ACR field trials are occurring at multiple sites in the Cairns-Port Douglas region through Reef stewardship activities involving GBR tourism operators, Traditional Owners, and not-for-profit organisations. It is hypothesised that these field trials and the presence of ACR devices at reef tourism sites do not negatively affect visitor experiences, and when accompanied by appropriate educational information, can potentially help to raise awareness of Reef stewardship and conservation efforts. We tested these hypotheses using a survey of 708 Reef visitors on five tourism vessels, 346 of whom reported observing ACR devices in situ during their coral reef experience. Ordinal regression tests of survey responses found no statistical relationship between respondents’ observation of ACR devices and (i) their overall Reef trip satisfaction, (ii) the perceived aesthetic beauty of the site(s) they visited, and (iii) their concern about the future health of the GBR. However, Reef visitors who observed ACR devices showed significantly lower levels of concern about the use of these devices on the Reef. The perceived quality of educational information presented to respondents was among the significant factors associated with their reef trip satisfaction and perceived beauty of reef sites. Our findings have implications for ACR practitioners and proponents who are concerned about public visibility, perceptions, and support for ACR initiatives, as the scale of such initiatives is expected to increase.

Failure to consider population structure when managing harvested fishes increases the risk of stock depletion, yet empirical estimates of population structure are often lacking for important fishery species. In this study, we characterise genetic variation in single nucleotide polymorphisms (SNPs) to assess population structure for three harvested species of tropical snappers across the broad (up to 300 km wide) and extensive (~ 4000 km) continental shelf of north-western Australia. Comparisons across ~ 300 individuals per species, showed remarkably similar patterns of genetic structure among Lutjanus sebae (red emperor), L. malabaricus (saddletail snapper) and Pristipomoides multidens (goldband snapper) despite subtle differences in biological and ecological traits. Low levels of genetic subdivision were reflected in an isolation by distance relationship where genetic connectivity increased with geographic proximity. This indicates extensive but not unlimited dispersal across the north-western Australian shelf. Our findings provide evidence of connectivity between current management areas, violating the assumption of multiple independent stocks. Spatial stock assessment models may be more suitable for the management of these species however demographic connectivity rates cannot be accurately estimated from the conventional population genetic approaches applied in this study. We recommend that managers aim to maintain adequate spawning biomass across current management areas, and assess stocks at finer scales, where practical. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-024-77424-4.

The reproducibility in microbiome studies is limited due to the lack of one gold-standard operating procedure. The aim of this study was to examine the impact of protocol variations on microbiome composition using metagenomic data sets from a single center. We assessed the variation in a data set consisted of 2,722 subjects, including 9 subcohorts harboring healthy subjects and patients with various disorders, such as inflammatory bowel disease, colorectal cancer, and type 2 diabetes. Two different DNA extraction kits, with or without lyticase, and two sample storage methods were compared. Our results indicated that DNA extraction had the largest impact on gut microbiota diversity among all host factors and sample operating procedures. Healthy subjects matched by age, body mass index, and sample operating methods exhibited reduced, yet significant differences (PERMANOVA, P < 0.05) in gut microbiota composition across studies. The variations contributed by DNA extraction were primarily driven by different recovery efficiency of gram-positive bacteria, e.g., phyla Firmicutes and Actinobacteria. This was further confirmed by a parallel comparison of fecal samples from five healthy subjects and a standard mock community. In addition, the DNA extraction method influenced DNA biomass, quality, and the detection of specific lineage-associated diseases. Sample operating approach and batch effects should be considered for cohorts with large sample size or longitudinal cohorts to ensure that source data were appropriately generated and analyzed. Comparison between samples processed with inconsistent methods should be dealt with caution. This study will promote the establishment of a sample operating standard to enhance our understanding of microbiome and translating in clinical practice. IMPORTANCE The reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 fecal samples generated from a single research center to examine the extent to which sample storage and DNA extraction influence the quantification of microbial composition and compared this variable with other sources of technical and biological variation. Our research highlights the impact of DNA extraction methods when analyzing microbiome data and suggests that the microbiome profile may be influenced by differences in the extraction efficiency of bacterial species. With metagenomics sequencing being increasingly used in clinical biology, our findings provide insight into the challenges using metagenomics sequencing in clinical diagnostics, where the detection of certain species and its abundance relative to a “healthy reference” is key.

A critical component of ecosystem restoration projects involves using genetic data to select source material that will enhance success under current and future climates. However, the complexity and expense of applying genetic data is a barrier to its use outside of specialised scientific contexts. To help overcome this barrier, we developed Reef Adapt (www.reefadapt.org), an innovative, globally applicable and expandable web platform that incorporates genetic, biophysical and environmental prediction data into marine restoration and assisted gene flow planning. The Reef Adapt tool provides maps that identify areas with populations suited to user-specified restoration/recipient sites under current and future climate scenarios. We demonstrate its versatility and practicality with four case studies of ecologically and evolutionarily diverse taxa: the habitat-forming corals Pocillopora damicornis and Acropora kenti, and macroalgae Phyllospora comosa and Ecklonia radiata. Reef Adapt is a management-ready tool to aid restoration and conservation efforts amidst ongoing habitat degradation and climate change.

Aim Identifying the maximum coral cover that a coral community can sustain (i.e., its ‘upper limit’) is important for predicting community dynamics and improving management strategies. Here, we quantify the relationship between estimated upper limits and key environmental factors on coral reefs: hard substrate availability, temperature and water clarity. Location Great Barrier Reef (GBR), Australia (over 1400 km). Time Period 1990 to 2022. Major Taxa Studied Scleractinian corals. Methods We used 32 years of data on coral cover around reef perimeters. Each reef was divided into four wave‐exposure habitats depending on prevailing wind conditions. For each site, we determined if hard coral cover had reached a plateau or upper limit. Next, we extracted existing estimates of hard substrate availability, modelled water temperature and Secchi depth. Then, we quantified the relationship between these environmental variables and the upper limits. Results We found varying upper limits across the GBR, with a median of 33% coral cover and only 17% of the estimated upper limits exceeded 50% coral cover. Upper limits increased towards the southern reefs. Our results show that upper limits increased with increasing hard substrate availability and decreased with temperature and, to a lesser extent, with water clarity. Main Conclusions The upper limits estimated in this study are much lower than what is commonly assumed when modelling ecological dynamics, most likely resulting in predicted recovery rates being inappropriately high. Although hard substrate ultimately restricted upper limits, there are mechanisms constraining the proportion of hard substrate that is covered by hard corals. The negative relationship between temperature and upper limits cannot be explained by changes in macroalgal abundance but may be related to changes in species composition. The quantitative relationships between the upper limits of coral cover and environmental variables will provide critical information to prioritise sites for management interventions.

Out‐planting corals onto coral reefs as a mechanism to increase coral cover on degraded reef systems is an increasing global activity. Current practices typically focus on asexual out‐planting of coral fragments (coral gardening). Newer sexual reproductive approaches are being developed to out‐plant younger corals produced in aquaculture facilities or sea‐based rearing pools to enable assisted evolution or assisted gene flow conservation genetics approaches. Designing out‐planting deployment operations requires decisions to be made on planting density and location in order to maximize future recruitment on both the out‐planted reefs, and on nearby reefs that are connected through oceanographic transport processes. The thinking presented here seeks to unpack how out‐planting density may be influenced, especially by local oceanographic conditions, in order to guide practitioners undertaking restoration projects.

Natural systems exhibit high spatial variability across multiple scales. Models that can capture ecosystem dynamics across space and time by explicitly incorporating major biological mechanisms are crucial, both for management and for ecological insight. In the case of coral reef systems, much focus has been on modelling variability between reefs, despite substantial variability also existing within reefs. We developed C~scape, a coral metacommunity modelling framework that integrates the demography of corals with population-level responses to physical and environmental spatial layers, to facilitate spatiotemporal predictions of coral dynamics across reefs at fine (100s of metres to kilometres) scales. We used satellite-derived habitat maps to modulate community growth spatially, as a proxy for the many interacting physical and environmental factors—e.g., depth, light, wave exposure, temperature, and substrate type—that drive within-reef variability in coral demography. With a case study from the Great Barrier Reef, we demonstrate the model’s capability for producing hindcasts of coral cover dynamics and show that overlooking within-reef variability may lead to misleading conclusions about metacommunity dynamics. C~scape provides a valuable framework for exploring a range of management and restoration scenarios at relevant spatial scales.

The functioning and richness of marine systems (and biological interactions such as parasitism) are continuously influenced by a changing environment. Using hierarchical modelling of species communities (HMSC), the presence and abundance of multiple parasite species of the black-spotted croaker, Protonibea diacanthus (Sciaenidae), was modelled against environmental measures reflecting seasonal change. Protonibea diacanthus were collected in three seasons across 2019–2021 from four locations within the waters of the Northern Territory, Australia. The length of P. diacanthus proved to have a strong positive effect on the abundance of parasite taxa and overall parasitic assemblage of the sciaenid host. This finding introduces potential implications for parasitism in the future as fish body size responds to fishing pressure and climate changes. Of the various environmental factors measured during the tropical seasons of northern Australia, water temperature and salinity changes were shown as potential causal factors for the variance in parasite presence and abundance, with changes most influential on external parasitic organisms. As environmental factors like ocean temperature and salinity directly affect parasite–host relationships, this study suggests that parasite assemblages and the ecological functions that they perform are likely to change considerably over the coming decades in response to climate change and its proceeding effects.